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Kalizang'oma A, Swarthout TD, Mwalukomo TS, Kamng'ona A, Brown C, Msefula J, Demetriou H, Chan JM, Roalfe L, Obolski U, Lourenço J, Goldblatt D, Chaguza C, French N, Heyderman RS. Clonal Expansion of a Streptococcus pneumoniae Serotype 3 Capsule Variant Sequence Type 700 With Enhanced Vaccine Escape Potential After 13-Valent Pneumococcal Conjugate Vaccine Introduction. J Infect Dis 2024:jiae040. [PMID: 38530917 DOI: 10.1093/infdis/jiae040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 01/21/2024] [Indexed: 03/28/2024] Open
Abstract
BACKGROUND Streptococcus pneumoniae serotype 3 remains a problem globally. Malawi introduced 13-valent pneumococcal conjugate vaccine (PCV13) in 2011, but there has been no direct protection against serotype 3 carriage. We explored whether vaccine escape by serotype 3 is due to clonal expansion of a lineage with a competitive advantage. METHODS The distribution of serotype 3 Global Pneumococcal Sequence Clusters (GPSCs) and sequence types (STs) globally was assessed using sequences from the Global Pneumococcal Sequencing Project. Whole-genome sequences of 135 serotype 3 carriage isolates from Blantyre, Malawi (2015-2019) were analyzed. Comparative analysis of the capsule locus, entire genomes, antimicrobial resistance, and phylogenetic reconstructions were undertaken. Opsonophagocytosis was evaluated using serum samples from vaccinated adults and children. RESULTS Serotype 3 GPSC10-ST700 isolates were most prominent in Malawi. Compared with the prototypical serotype 3 capsular polysaccharide locus sequence, 6 genes are absent, with retention of capsule polysaccharide biosynthesis. This lineage is characterized by increased antimicrobial resistance and lower susceptibility to opsonophagocytic killing. CONCLUSIONS A serotype 3 variant in Malawi has genotypic and phenotypic characteristics that could enhance vaccine escape and clonal expansion after post-PCV13 introduction. Genomic surveillance among high-burden populations is essential to improve the effectiveness of next-generation pneumococcal vaccines.
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Affiliation(s)
- Akuzike Kalizang'oma
- NIHR Mucosal Pathogens Research Unit, Research Department of Infection, Division of Infection and Immunity, University College London, London, United Kingdom
- Pneumonia and Meningitis Pathogens Associate Research Group, Malawi-Liverpool-Wellcome Research Programme, Blantyre, Malawi
| | - Todd D Swarthout
- NIHR Mucosal Pathogens Research Unit, Research Department of Infection, Division of Infection and Immunity, University College London, London, United Kingdom
- Pneumonia and Meningitis Pathogens Associate Research Group, Malawi-Liverpool-Wellcome Research Programme, Blantyre, Malawi
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Thandie S Mwalukomo
- School of Medicine and Oral Health, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Arox Kamng'ona
- School of Life Sciences and Allied Health Professionals, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Comfort Brown
- Pneumonia and Meningitis Pathogens Associate Research Group, Malawi-Liverpool-Wellcome Research Programme, Blantyre, Malawi
| | - Jacquline Msefula
- Pneumonia and Meningitis Pathogens Associate Research Group, Malawi-Liverpool-Wellcome Research Programme, Blantyre, Malawi
| | - Hayley Demetriou
- Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Jia Mun Chan
- NIHR Mucosal Pathogens Research Unit, Research Department of Infection, Division of Infection and Immunity, University College London, London, United Kingdom
| | - Lucy Roalfe
- Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Uri Obolski
- Porter School of the Environment and Earth Science, Tel-Aviv University, Tel-Aviv, Israel
| | - Jose Lourenço
- Faculdade de Ciências, BioISI, Universidade de Lisboa, Lisbon, Portugal
| | - David Goldblatt
- NIHR Mucosal Pathogens Research Unit, Research Department of Infection, Division of Infection and Immunity, University College London, London, United Kingdom
- Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Chrispin Chaguza
- NIHR Mucosal Pathogens Research Unit, Research Department of Infection, Division of Infection and Immunity, University College London, London, United Kingdom
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, Connecticut, USA
- Yale Institute for Global Health, Yale University, New Haven, Connecticut, USA
| | - Neil French
- Institute of Infection, Veterinary and Ecological Sciences, Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, United Kingdom
| | - Robert S Heyderman
- NIHR Mucosal Pathogens Research Unit, Research Department of Infection, Division of Infection and Immunity, University College London, London, United Kingdom
- Pneumonia and Meningitis Pathogens Associate Research Group, Malawi-Liverpool-Wellcome Research Programme, Blantyre, Malawi
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Doherty K, Dula D, Chirwa A, Nsomba E, Nkhoma VS, Toto N, Chikaonda T, Kamng'ona R, Phiri J, Reiné J, Ndaferankhande J, Makhaza L, Banda P, Jambo K, Ferreira DM, Gordon SB. Experimental pneumococcal carriage in people living with HIV in Malawi: the first controlled human infection model in a key at-risk population. Wellcome Open Res 2024; 9:2. [PMID: 38362541 PMCID: PMC10864820 DOI: 10.12688/wellcomeopenres.19949.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/03/2023] [Indexed: 02/17/2024] Open
Abstract
Background: As well as suffering a high burden of pneumococcal disease people living with HIV (PLHIV) may contribute to community transmission in sub-Saharan African (sSA) settings. Pneumococcal vaccination is not currently offered to PLHIV in sSA but may prevent disease and reduce transmission. More evidence of vaccine effectiveness against carriage in PLHIV is needed. An Experimental Human Pneumococcal Carriage model (EHPC) has been safely and acceptably used in healthy adults in Malawi to evaluate pneumococcal vaccines against carriage and to identify immune correlates of protection from carriage. This study will establish the same model in PLHIV and will be the first controlled human infection model (CHIM) in this key population. Methods: Healthy participants with and without HIV will be inoculated intranasally with Streptococcus pneumoniae serotype 6B. Sequential cohorts will be challenged with increasing doses to determine the optimal safe challenge dose to establish experimental carriage. Nasal fluid, nasal mucosal, and blood samples will be taken before inoculation and on days 2, 7, 14, and 21 following inoculation to measure pneumococcal carriage density and identify immune correlates of protection from carriage. The vast majority of natural pneumococcal carriage events in PLHIV do not result in invasive disease and no invasive disease is expected in this study. However, robust participant safety monitoring is designed to identify signs of invasive disease early should they develop, and to implement treatment immediately. Participants will complete a Likert-style questionnaire at study-end to establish acceptability. Interpretations: We expect the EHPC model to be safely and acceptably implemented in PLHIV. The CHIM can then be used to accelerate pneumococcal vaccine evaluations in this population, and an evidence-based pneumococcal vaccination policy for PLHIV in sSA.
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Affiliation(s)
- Klara Doherty
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Southern Region, Malawi
- Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
| | - Dingase Dula
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Southern Region, Malawi
| | - Anthony Chirwa
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Southern Region, Malawi
| | - Edna Nsomba
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Southern Region, Malawi
| | - Vitumbiko S. Nkhoma
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Southern Region, Malawi
| | - Neema Toto
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Southern Region, Malawi
| | - Tarsizio Chikaonda
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Southern Region, Malawi
| | - Raphael Kamng'ona
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Southern Region, Malawi
| | - Joseph Phiri
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Southern Region, Malawi
| | - Jesús Reiné
- Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
- Oxford Vaccine Group, University of Oxford, Oxford, England, UK
| | - John Ndaferankhande
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Southern Region, Malawi
| | - Lumbani Makhaza
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Southern Region, Malawi
| | - Peter Banda
- Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Kondwani Jambo
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Southern Region, Malawi
- Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
| | - Daniela M Ferreira
- Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
- Oxford Vaccine Group, University of Oxford, Oxford, England, UK
| | - Stephen B Gordon
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Southern Region, Malawi
- Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
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3
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Senok A, Thomsen J, Abdulrazzaq NM, Menezes GA, Ayoub Moubareck C, Everett D. Antimicrobial resistance in Streptococcus pneumoniae: a retrospective analysis of emerging trends in the United Arab Emirates from 2010 to 2021. Front Public Health 2023; 11:1244357. [PMID: 38074724 PMCID: PMC10702210 DOI: 10.3389/fpubh.2023.1244357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 10/24/2023] [Indexed: 12/18/2023] Open
Abstract
Introduction Although pneumococcal conjugate vaccines (PCV) have been effective in reducing the burden of Streptococcus pneumoniae infections, there is a paucity of data on the relationship with antimicrobial resistance (AMR) trends in the Arabian Gulf region. This study was carried out to assess S. pneumoniae resistance trends in the United Arab Emirates (UAE) where PCV-13 vaccination was introduced in 2011. Methods Retrospective analysis of S. pneumoniae demographic and microbiological data collected as part of the national AMR surveillance program from 2010 to 2021 was carried out. A survey of reporting sites and hand searching of annual reports of local health authorities was carried out to identify data on S. pneumoniae serotypes as this is not included in the AMR surveillance database. Results From 2010 to 2021, 11,242 non-duplicate S. pneumoniae isolates were reported, increasing from 324 in 2010 to 1,115 in 2021. Factoring in annual increment in the number of surveillance sites, the number of isolates per site showed an upward trajectory from 2015 to 2018 and declined in 2020 with the onset of the pandemic. The majority of isolates (n/N = 5,751/11,242; 51.2%) were from respiratory tract specimens with 44.5% (n/N = 2,557/5,751) being nasal colonizers. Up to 11.9% (n/N = 1,337/11,242) were invasive pneumococcal disease (IPD) isolates obtained from sterile site specimens including blood (n = 1,262), cerebrospinal (n = 52), pleural (n = 19) and joint (n = 4) fluid; and were predominantly from pediatric patients. The downward trend for amoxicillin and for penicillin G at the non-meningitis and meningitis as well as oral penicillin breakpoints was statistically significant. In contrast, increasing trends of resistance were seen for levofloxacin, moxifloxacin, trimethoprim/sulfamethoxazole and erythromycin. IPD and non-IPD isolates showed similar demographic and AMR trends. None of the surveillance sites carried out S. pneumoniae serotyping and handsearching of annual reports did not yield this information. Conclusion The increasing trend of pneumococcal disease and AMR with emergence of isolates with MDR phenotype despite is of concern. In the absence of S. pneumoniae serotyping the role of non-vaccine serotypes in driving this pattern remains unknown. There is an urgent need for serotype, genomic and AMR surveillance of S. pneumoniae isolates in the UAE.
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Affiliation(s)
- Abiola Senok
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
- School of Dentistry, Cardiff University, Cardiff, United Kingdom
| | - Jens Thomsen
- Abu Dhabi Public Health Center, Abu Dhabi, United Arab Emirates
- Department of Pathology and Infectious Diseases, Khalifa University, Abu Dhabi, United Arab Emirates
| | - Najiba M. Abdulrazzaq
- Al Kuwait Hospital Dubai, Emirates Health Establishment, Dubai, United Arab Emirates
- Public Health Sector, Ministry of Health and Prevention, Dubai, United Arab Emirates
| | | | - Godfred Antony Menezes
- Department of Medical Microbiology and Immunology, RAK Medical and Health Sciences University, Ras Al-Khaimah, United Arab Emirates
| | | | - Dean Everett
- Department of Pathology and Infectious Diseases, Khalifa University, Abu Dhabi, United Arab Emirates
- Biotechnology Center, Khalifa University, Abu Dhabi, United Arab Emirates
- Infection Research Unit, Khalifa University, Abu Dhabi, United Arab Emirates
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Obolski U, Swarthout TD, Kalizang'oma A, Mwalukomo TS, Chan JM, Weight CM, Brown C, Cave R, Cornick J, Kamng'ona AW, Msefula J, Ercoli G, Brown JS, Lourenço J, Maiden MC, French N, Gupta S, Heyderman RS. The metabolic, virulence and antimicrobial resistance profiles of colonising Streptococcus pneumoniae shift after PCV13 introduction in urban Malawi. Nat Commun 2023; 14:7477. [PMID: 37978177 PMCID: PMC10656543 DOI: 10.1038/s41467-023-43160-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 11/02/2023] [Indexed: 11/19/2023] Open
Abstract
Streptococcus pneumoniae causes substantial mortality among children under 5-years-old worldwide. Polysaccharide conjugate vaccines (PCVs) are highly effective at reducing vaccine serotype disease, but emergence of non-vaccine serotypes and persistent nasopharyngeal carriage threaten this success. We investigated the hypothesis that following vaccine, adapted pneumococcal genotypes emerge with the potential for vaccine escape. We genome sequenced 2804 penumococcal isolates, collected 4-8 years after introduction of PCV13 in Blantyre, Malawi. We developed a pipeline to cluster the pneumococcal population based on metabolic core genes into "Metabolic genotypes" (MTs). We show that S. pneumoniae population genetics are characterised by emergence of MTs with distinct virulence and antimicrobial resistance (AMR) profiles. Preliminary in vitro and murine experiments revealed that representative isolates from emerging MTs differed in growth, haemolytic, epithelial infection, and murine colonisation characteristics. Our results suggest that in the context of PCV13 introduction, pneumococcal population dynamics had shifted, a phenomenon that could further undermine vaccine control and promote spread of AMR.
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Affiliation(s)
- Uri Obolski
- Department of Epidemiology and Preventive Medicine, School of Public Health, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
- Porter School of the Environment and Earth Sciences, Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel.
| | - Todd D Swarthout
- Malawi Liverpool Wellcome Programme, Blantyre, Malawi
- Mucosal Pathogens Research Group, Research Department of Infection, Division of Infection & Immunity, University College London, London, United Kingdom
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, Netherlands
| | - Akuzike Kalizang'oma
- Malawi Liverpool Wellcome Programme, Blantyre, Malawi
- Mucosal Pathogens Research Group, Research Department of Infection, Division of Infection & Immunity, University College London, London, United Kingdom
| | | | - Jia Mun Chan
- Mucosal Pathogens Research Group, Research Department of Infection, Division of Infection & Immunity, University College London, London, United Kingdom
| | - Caroline M Weight
- Mucosal Pathogens Research Group, Research Department of Infection, Division of Infection & Immunity, University College London, London, United Kingdom
- Faculty of Health and Medicine, Biomedical and Life Sciences, Lancaster University, Lancaster, United Kingdom
- Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, United Kingdom
| | - Comfort Brown
- Malawi Liverpool Wellcome Programme, Blantyre, Malawi
| | - Rory Cave
- Mucosal Pathogens Research Group, Research Department of Infection, Division of Infection & Immunity, University College London, London, United Kingdom
| | - Jen Cornick
- Malawi Liverpool Wellcome Programme, Blantyre, Malawi
- Clinical Infection, Microbiology and Immunology, Institute of Infection Veterinary & Ecological Science, University of Liverpool, Liverpool, United Kingdom
| | | | | | - Giuseppe Ercoli
- UCL Respiratory, Division of Medicine, University College London, London, United Kingdom
| | - Jeremy S Brown
- UCL Respiratory, Division of Medicine, University College London, London, United Kingdom
| | - José Lourenço
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Universidade Católica Portuguesa, Faculty of Medicine, Biomedical Research Centre, Lisbon, Portugal
| | - Martin C Maiden
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Neil French
- Clinical Infection, Microbiology and Immunology, Institute of Infection Veterinary & Ecological Science, University of Liverpool, Liverpool, United Kingdom
| | - Sunetra Gupta
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Robert S Heyderman
- Malawi Liverpool Wellcome Programme, Blantyre, Malawi.
- Mucosal Pathogens Research Group, Research Department of Infection, Division of Infection & Immunity, University College London, London, United Kingdom.
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5
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Elfving K, Strömberg LG, Geravandi S, Andersson M, Bachelard M, Msellem M, Shakely D, Trollfors B, Nordén R, Mårtensson A, Björkman A, Lindh M. Pneumococcal concentration and serotype distribution in preschool children with radiologically confirmed pneumonia compared to healthy controls prior to introduction of pneumococcal vaccination in Zanzibar: an observational study. BMC Infect Dis 2022; 22:925. [PMID: 36496395 PMCID: PMC9737767 DOI: 10.1186/s12879-022-07902-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 11/29/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The World Health Organization recommends pneumococcal vaccination (PCV) in the first year of life. We investigated pneumococcal serotypes in children with clinical or radiologically confirmed pneumonia and healthy controls prior to PCV13 vaccine introduction in Zanzibar. METHODS Children (n = 677) with non-severe acute febrile illness aged 2-59 months presenting to a health centre in Zanzibar, Tanzania April-July 2011 were included. Nasopharyngeal swabs collected at enrolment were analysed by real-time PCR to detect and quantify pneumococcal serotypes in patients (n = 648) and in healthy asymptomatic community controls (n = 161). Children with clinical signs of pneumonia according to the Integrated Management of Childhood illness guidelines ("IMCI pneumonia") were subjected to a chest-X-ray. Consolidation on chest X-ray was considered "radiological pneumonia". RESULTS Pneumococcal DNA was detected in the nasopharynx of 562/809 (69%) children (70% in patients and 64% in healthy controls), with no significant difference in proportions between patients with or without presence of fever, malnutrition, IMCI pneumonia or radiological pneumonia. The mean pneumococcal concentration was similar in children with and without radiological pneumonia (Ct value 26.3 versus 27.0, respectively, p = 0.3115). At least one serotype could be determined in 423 (75%) participants positive for pneumococci of which 33% had multiple serotypes detected. A total of 23 different serotypes were identified. One serotype (19F) was more common in children with fever (86/648, 13%) than in healthy controls (12/161, 7%), (p = 0.043). Logistic regression adjusting for age and gender showed that serotype 9A/V [aOR = 10.9 (CI 2.0-60.0, p = 0.006)] and 14 [aOR = 3.9 (CI 1.4-11.0, p = 0.012)] were associated with radiological pneumonia. The serotypes included in the PCV13 vaccine were found in 376 (89%) of the 423 serotype positive participants. CONCLUSION The PCV13 vaccine introduced in 2012 targets a great majority of the identified serotypes. Infections with multiple serotypes are common. PCR-determined concentrations of pneumococci in nasopharynx were not associated with radiologically confirmed pneumonia. Trial registration Clinicaltrials.gov (NCT01094431).
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Affiliation(s)
- Kristina Elfving
- grid.8761.80000 0000 9919 9582School of Public Health and Community Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Göteborg, Sweden ,grid.8761.80000 0000 9919 9582Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Göteborg, Sweden ,grid.8761.80000 0000 9919 9582Department of Pediatrics, Sahlgrenska Academy, University of Gothenburg, Göteborg, Sweden
| | - Lucia Gonzales Strömberg
- grid.8761.80000 0000 9919 9582Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Göteborg, Sweden
| | - Shadi Geravandi
- grid.8761.80000 0000 9919 9582Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Göteborg, Sweden
| | - Maria Andersson
- grid.8761.80000 0000 9919 9582Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Göteborg, Sweden ,grid.1649.a000000009445082XDepartment of Clinical Microbiology, Sahlgrenska University Hospital, Göteborg, Sweden
| | - Marc Bachelard
- grid.8761.80000 0000 9919 9582Department of Pediatrics, Sahlgrenska Academy, University of Gothenburg, Göteborg, Sweden
| | - Mwinyi Msellem
- grid.415734.00000 0001 2185 2147Department of Planning, Policy and Research, Ministry of Health, Zanzibar, Tanzania
| | - Delér Shakely
- grid.8761.80000 0000 9919 9582School of Public Health and Community Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Göteborg, Sweden
| | - Birger Trollfors
- grid.8761.80000 0000 9919 9582Department of Pediatrics, Sahlgrenska Academy, University of Gothenburg, Göteborg, Sweden
| | - Rickard Nordén
- grid.8761.80000 0000 9919 9582Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Göteborg, Sweden ,grid.1649.a000000009445082XDepartment of Clinical Microbiology, Sahlgrenska University Hospital, Göteborg, Sweden
| | - Andreas Mårtensson
- grid.8993.b0000 0004 1936 9457Department of Women’s and Children’s Health, International Maternal and Child Health (IMCH), Uppsala University, Uppsala, Sweden
| | - Anders Björkman
- grid.4714.60000 0004 1937 0626Malaria Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Solna, Sweden
| | - Magnus Lindh
- grid.8761.80000 0000 9919 9582Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Göteborg, Sweden ,grid.1649.a000000009445082XDepartment of Clinical Microbiology, Sahlgrenska University Hospital, Göteborg, Sweden
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Chaguza C, Yang M, Jacques LC, Bentley SD, Kadioglu A. Serotype 1 pneumococcus: epidemiology, genomics, and disease mechanisms. Trends Microbiol 2022; 30:581-592. [PMID: 34949516 PMCID: PMC7613904 DOI: 10.1016/j.tim.2021.11.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 11/05/2021] [Accepted: 11/08/2021] [Indexed: 12/14/2022]
Abstract
Streptococcus pneumoniae (the 'pneumococcus') is a significant cause of morbidity and mortality worldwide, causing life-threatening diseases such as pneumonia, bacteraemia, and meningitis, with an annual death burden of over one million. Discovered over a century ago, pneumococcal serotype 1 (S1) is a significant cause of these life-threatening diseases. Our understanding of the epidemiology and biology of pneumococcal S1 has significantly improved over the past two decades, informing the development of preventative and surveillance strategies. However, many questions remain unanswered. Here, we review the current state of knowledge of pneumococcal S1, with a special emphasis on clinical epidemiology, genomics, and disease mechanisms.
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Affiliation(s)
- Chrispin Chaguza
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK; Darwin College, University of Cambridge, Silver Street, Cambridge, UK; Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, The Ronald Ross Building, West Derby St, Liverpool, UK; NIHR Mucosal Pathogens Research Unit, Division of Infection and Immunity, University College London, London, UK.
| | - Marie Yang
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, The Ronald Ross Building, West Derby St, Liverpool, UK
| | - Laura C Jacques
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, The Ronald Ross Building, West Derby St, Liverpool, UK.
| | - Stephen D Bentley
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK; Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, The Ronald Ross Building, West Derby St, Liverpool, UK; Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, UK
| | - Aras Kadioglu
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, The Ronald Ross Building, West Derby St, Liverpool, UK
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Almeida SCG, Lo SW, Hawkins PA, Gladstone RA, Cassiolato AP, Klugman KP, Breiman RF, Bentley SD, McGee L, Brandileone MCDC. Genomic surveillance of invasive Streptococcus pneumoniae isolates in the period pre-PCV10 and post-PCV10 introduction in Brazil. Microb Genom 2021; 7. [PMID: 34609274 PMCID: PMC8627213 DOI: 10.1099/mgen.0.000635] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
In 2010, Brazil introduced the 10-valent pneumococcal conjugate vaccine (PCV10) into the national children’s immunization programme. This study describes the genetic characteristics of invasive Streptococcus pneumoniae isolates before and after PCV10 introduction. A subset of 466 [pre-PCV10 (2008–2009): n=232, post-PCV10 (2012–2013): n=234;<5 years old: n=310, ≥5 years old: n=156] pneumococcal isolates, collected through national laboratory surveillance, were whole-genome sequenced (WGS) to determine serotype, pilus locus, antimicrobial resistance and genetic lineages. Following PCV10 introduction, in the <5 years age group, non-vaccine serotypes (NVT) serotype 3 and serotype 19A were the most frequent, and serotypes 12F, 8 and 9 N in the ≥5 years old group. The study identified 65 Global Pneumococcal Sequence Clusters (GPSCs): 49 (88 %) were GPSCs previously described and 16 (12 %) were Brazilian clusters. In total, 36 GPSCs (55 %) were NVT lineages, 18 (28 %) vaccine serotypes (VT) and 11 (17 %) were both VT and NVT lineages. In both sampling periods, the most frequent lineage was GPSC6 (CC156, serotypes 14/9V). In the <5 years old group, a decrease in penicillin (P=0.0123) and cotrimoxazole (P<0.0001) resistance and an increase in tetracycline (P=0.019) were observed. Penicillin nonsusceptibility was predicted in 40 % of the isolates; 127 PBP combinations were identified (51 predicted MIC≥0.125 mg l−1); cotrimoxazole (folA and/or folP alterations), macrolide (mef and/or ermB) and tetracycline (tetM, tetO or tetS/M) resistance were predicted in 63, 13 and 21.6 % of pneumococci studied, respectively. The main lineages associated with multidrug resistance in the post-PCV10 period were composed of NVT, GPSC1 (CC320, serotype 19A), and GPSC47 (ST386, serotype 6C). The study provides a baseline for future comparisons and identified important NVT lineages in the post-PCV10 period in Brazil.
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Affiliation(s)
- Samanta C. G. Almeida
- National Reference Laboratory for Meningitis and Pneumococcal Infections, Institute Adolfo Lutz, São Paulo, Brazil
- *Correspondence: Samanta C. G. Almeida,
| | - Stephanie W. Lo
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Paulina A. Hawkins
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, USA
| | | | - Ana Paula Cassiolato
- National Reference Laboratory for Meningitis and Pneumococcal Infections, Institute Adolfo Lutz, São Paulo, Brazil
| | - Keith P. Klugman
- Emeritus Professor of Global Health, Emory University, Atlanta, GA, USA
| | | | - Stephen D. Bentley
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Lesley McGee
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, USA
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Kalizang'oma A, Chaguza C, Gori A, Davison C, Beleza S, Antonio M, Beall B, Goldblatt D, Kwambana-Adams B, Bentley SD, Heyderman RS. Streptococcus pneumoniae serotypes that frequently colonise the human nasopharynx are common recipients of penicillin-binding protein gene fragments from Streptococcus mitis. Microb Genom 2021; 7. [PMID: 34550067 PMCID: PMC8715442 DOI: 10.1099/mgen.0.000622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Streptococcus pneumoniae is an important global pathogen that causes bacterial pneumonia, sepsis and meningitis. Beta-lactam antibiotics are the first-line treatment for pneumococcal disease, however, their effectiveness is hampered by beta-lactam resistance facilitated by horizontal genetic transfer (HGT) with closely related species. Although interspecies HGT is known to occur among the species of the genus Streptococcus, the rates and effects of HGT between Streptococcus pneumoniae and its close relatives involving the penicillin binding protein (pbp) genes remain poorly understood. Here we applied the fastGEAR tool to investigate interspecies HGT in pbp genes using a global collection of whole-genome sequences of Streptococcus mitis, Streptococcus oralis and S. pneumoniae. With these data, we established that pneumococcal serotypes 6A, 13, 14, 16F, 19A, 19F, 23F and 35B were the highest-ranking serotypes with acquired pbp fragments. S. mitis was a more frequent pneumococcal donor of pbp fragments and a source of higher pbp nucleotide diversity when compared with S. oralis. Pneumococci that acquired pbp fragments were associated with a higher minimum inhibitory concentration (MIC) for penicillin compared with pneumococci without acquired fragments. Together these data indicate that S. mitis contributes to reduced β-lactam susceptibility among commonly carried pneumococcal serotypes that are associated with long carriage duration and high recombination frequencies. As pneumococcal vaccine programmes mature, placing increasing pressure on the pneumococcal population structure, it will be important to monitor the influence of antimicrobial resistance HGT from commensal streptococci such as S. mitis.
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Affiliation(s)
- Akuzike Kalizang'oma
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection & Immunity, University College London, London, UK
| | - Chrispin Chaguza
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK.,Darwin College, University of Cambridge, Silver Street, Cambridge, UK.,Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Andrea Gori
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection & Immunity, University College London, London, UK
| | - Charlotte Davison
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Sandra Beleza
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Martin Antonio
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, World Health Organization, Collaborating Centre for New Vaccines Surveillance, Banjul, Gambia
| | - Bernard Beall
- Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Division of Bacterial Diseases, Atlanta, GA, USA
| | - David Goldblatt
- University College London, Great Ormond Street Institute of Child Health, London, UK
| | - Brenda Kwambana-Adams
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection & Immunity, University College London, London, UK
| | | | - Robert S Heyderman
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection & Immunity, University College London, London, UK
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9
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D'Aeth JC, van der Linden MPG, McGee L, de Lencastre H, Turner P, Song JH, Lo SW, Gladstone RA, Sá-Leão R, Ko KS, Hanage WP, Breiman RF, Beall B, Bentley SD, Croucher NJ. The role of interspecies recombination in the evolution of antibiotic-resistant pneumococci. eLife 2021; 10:e67113. [PMID: 34259624 PMCID: PMC8321556 DOI: 10.7554/elife.67113] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/16/2021] [Indexed: 12/27/2022] Open
Abstract
Multidrug-resistant Streptococcus pneumoniae emerge through the modification of core genome loci by interspecies homologous recombinations, and acquisition of gene cassettes. Both occurred in the otherwise contrasting histories of the antibiotic-resistant S. pneumoniae lineages PMEN3 and PMEN9. A single PMEN3 clade spread globally, evading vaccine-induced immunity through frequent serotype switching, whereas locally circulating PMEN9 clades independently gained resistance. Both lineages repeatedly integrated Tn916-type and Tn1207.1-type elements, conferring tetracycline and macrolide resistance, respectively, through homologous recombination importing sequences originating in other species. A species-wide dataset found over 100 instances of such interspecific acquisitions of resistance cassettes and flanking homologous arms. Phylodynamic analysis of the most commonly sampled Tn1207.1-type insertion in PMEN9, originating from a commensal and disrupting a competence gene, suggested its expansion across Germany was driven by a high ratio of macrolide-to-β-lactam consumption. Hence, selection from antibiotic consumption was sufficient for these atypically large recombinations to overcome species boundaries across the pneumococcal chromosome.
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Affiliation(s)
- Joshua C D'Aeth
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College LondonLondonUnited Kingdom
| | - Mark PG van der Linden
- Institute for Medical Microbiology, National Reference Center for Streptococci, University Hospital RWTH AachenAachenGermany
| | - Lesley McGee
- Respiratory Diseases Branch, Centers for Disease Control and PreventionAtlantaUnited States
| | - Herminia de Lencastre
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica, Universidade Nova de LisboaOeirasPortugal
- Laboratory of Microbiology and Infectious Diseases, The Rockefeller UniversityNew YorkUnited States
| | - Paul Turner
- Cambodia Oxford Medical Research Unit, Angkor Hospital for ChildrenSiem ReapCambodia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
| | - Jae-Hoon Song
- Department of Molecular Cell Biology, Sungkyunkwan University School of MedicineSuwonRepublic of Korea
| | - Stephanie W Lo
- Parasites & Microbes, Wellcome Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Rebecca A Gladstone
- Parasites & Microbes, Wellcome Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Raquel Sá-Leão
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica, Universidade Nova de LisboaOeirasPortugal
| | - Kwan Soo Ko
- Department of Molecular Cell Biology, Sungkyunkwan University School of MedicineSuwonRepublic of Korea
| | - William P Hanage
- Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public HealthBostonUnited States
| | - Robert F Breiman
- Department of Global Health, Rollins School of Public Health, Emory UniversityAtlantaUnited States
| | - Bernard Beall
- Respiratory Diseases Branch, Centers for Disease Control and PreventionAtlantaUnited States
| | - Stephen D Bentley
- Parasites & Microbes, Wellcome Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Nicholas J Croucher
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College LondonLondonUnited Kingdom
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10
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Lo SW, Gladstone RA, van Tonder AJ, Du Plessis M, Cornick JE, Hawkins PA, Madhi SA, Nzenze SA, Kandasamy R, Ravikumar KL, Elmdaghri N, Kwambana-Adams B, Almeida SCG, Skoczynska A, Egorova E, Titov L, Saha SK, Paragi M, Everett DB, Antonio M, Klugman KP, Li Y, Metcalf BJ, Beall B, McGee L, Breiman RF, Bentley SD, von Gottberg A. A mosaic tetracycline resistance gene tet(S/M) detected in an MDR pneumococcal CC230 lineage that underwent capsular switching in South Africa. J Antimicrob Chemother 2021; 75:512-520. [PMID: 31789384 PMCID: PMC7021099 DOI: 10.1093/jac/dkz477] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 09/26/2019] [Accepted: 10/16/2019] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES We reported tet(S/M) in Streptococcus pneumoniae and investigated its temporal spread in relation to nationwide clinical interventions. METHODS We whole-genome sequenced 12 254 pneumococcal isolates from 29 countries on an Illumina HiSeq sequencer. Serotype, multilocus ST and antibiotic resistance were inferred from genomes. An SNP tree was built using Gubbins. Temporal spread was reconstructed using a birth-death model. RESULTS We identified tet(S/M) in 131 pneumococcal isolates and none carried other known tet genes. Tetracycline susceptibility testing results were available for 121 tet(S/M)-positive isolates and all were resistant. A majority (74%) of tet(S/M)-positive isolates were from South Africa and caused invasive diseases among young children (59% HIV positive, where HIV status was available). All but two tet(S/M)-positive isolates belonged to clonal complex (CC) 230. A global phylogeny of CC230 (n=389) revealed that tet(S/M)-positive isolates formed a sublineage predicted to exhibit resistance to penicillin, co-trimoxazole, erythromycin and tetracycline. The birth-death model detected an unrecognized outbreak of this sublineage in South Africa between 2000 and 2004 with expected secondary infections (effective reproductive number, R) of ∼2.5. R declined to ∼1.0 in 2005 and <1.0 in 2012. The declining epidemic could be related to improved access to ART in 2004 and introduction of pneumococcal conjugate vaccine (PCV) in 2009. Capsular switching from vaccine serotype 14 to non-vaccine serotype 23A was observed within the sublineage. CONCLUSIONS The prevalence of tet(S/M) in pneumococci was low and its dissemination was due to an unrecognized outbreak of CC230 in South Africa. Capsular switching in this MDR sublineage highlighted its potential to continue to cause disease in the post-PCV13 era.
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Affiliation(s)
- Stephanie W Lo
- Parasites and Microbes Programme, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Rebecca A Gladstone
- Parasites and Microbes Programme, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Andries J van Tonder
- Parasites and Microbes Programme, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Mignon Du Plessis
- Centre for Respiratory Disease and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa.,School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Jennifer E Cornick
- Malawi Liverpool Wellcome Trust Clinical Research Programme, PO Box 30096, Blantyre, Malawi.,Institute of Infection & Global Health, University of Liverpool, Liverpool L69 7BE, UK
| | - Paulina A Hawkins
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Shabir A Madhi
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, Johannesburg, South Africa.,Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, Johannesburg, South Africa
| | - Susan A Nzenze
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, Johannesburg, South Africa.,Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, Johannesburg, South Africa
| | - Rama Kandasamy
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford OX3 9DU, UK
| | - K L Ravikumar
- Department of Microbiology, Kempegowda Institute of Medical Sciences Hospital & Research Centre, Bangalore, India
| | - Naima Elmdaghri
- Department of Microbiology, Faculty of Medicine and Pharmacy, B.P. 9154, Hassan II University of Casablanca, Casablanca, Morocco.,Bacteriology-Virology and Hospital Hygiene Laboratory, University Hospital Centre Ibn Rochd, Casablanca, Morocco
| | - Brenda Kwambana-Adams
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London, UK.,WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit, The Gambia at The London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Samanta Cristine Grassi Almeida
- National Laboratory for Meningitis and Pneumococcal Infections, Center of Bacteriology, Institute Adolfo Lutz (IAL), São Paulo, Brazil
| | - Anna Skoczynska
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Warsaw, Poland
| | - Ekaterina Egorova
- Laboratory of Clinical Microbiology and Biotechnology, Moscow Research Institute for Epidemiology and Microbiology, Moscow, Russian Federation
| | - Leonid Titov
- Laboratory of Clinical and Experimental Microbiology, The Republican Research and Practical Center for Epidemiology and Microbiology, Minsk, Belarus
| | - Samir K Saha
- Department of Microbiology, Dhaka Shishu (Children's) Hospital, Child Health Research Foundation, Dhaka, Bangladesh
| | - Metka Paragi
- Department for Public Health Microbiology, National Laboratory of Health, Environment and Food, Maribor, Slovenia
| | - Dean B Everett
- Malawi Liverpool Wellcome Trust Clinical Research Programme, PO Box 30096, Blantyre, Malawi.,University of Edinburgh, The Queens Medical Research Institute, Edinburgh EH16 4TJ, UK
| | - Martin Antonio
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit, The Gambia at The London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Keith P Klugman
- Centre for Respiratory Disease and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa.,School of Pathology, University of the Witwatersrand, Johannesburg, South Africa.,Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA.,Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Yuan Li
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Benjamin J Metcalf
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Bernard Beall
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Lesley McGee
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Robert F Breiman
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA.,Emory Global Health Institute, Emory University, Atlanta, GA 30322, USA
| | - Stephen D Bentley
- Parasites and Microbes Programme, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Anne von Gottberg
- Centre for Respiratory Disease and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa.,School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
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11
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Antibiotic Susceptibility of Staphylococcus aureus and Streptococcus pneumoniae Isolates from the Nasopharynx of Febrile Children under 5 Years in Nanoro, Burkina Faso. Antibiotics (Basel) 2021; 10:antibiotics10040444. [PMID: 33920987 PMCID: PMC8071235 DOI: 10.3390/antibiotics10040444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/07/2021] [Accepted: 04/13/2021] [Indexed: 11/17/2022] Open
Abstract
(1) Background: nasopharynx colonization by resistant Staphylococcus aureus and Streptococcus pneumoniae can lead to serious diseases. Emerging resistance to antibiotics commonly used to treat infections due to these pathogens poses a serious threat to the health system. The present study aimed to determine the antibiotic susceptibility of S. aureus and S. pneumoniae isolates from the febrile children’s nasopharynx under 5 years in Nanoro (Burkina Faso). (2) Methods: bacterial isolates were identified from nasopharyngeal swabs prospectively collected from 629 febrile children. Antibiotic susceptibility of S. aureus and S. pneumoniae isolates was assessed by Kirby–Bauer method and results were interpreted according to the Clinical and Laboratory Standard Institute guidelines. (3) Results: bacterial colonization was confirmed in 154 (24.5%) of children of whom 96.1% carried S. aureus, 3.2% had S. pneumoniae, and 0.6% carried both bacteria. S. aureus isolates showed alarming resistance to penicillin (96.0%) and S. pneumoniae was highly resistant to tetracycline (100%) and trimethoprim–sulfamethoxazole (83.3%), and moderately resistant to penicillin (50.0%). Furthermore, 4.0% of S. aureus identified were methicillin resistant. (4) Conclusion: this study showed concerning resistance rates to antibiotics to treat suspected bacterial respiratory tract infections. The work highlights the necessity to implement continuous antibiotic resistance surveillance.
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12
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Dzaraly ND, Mohd Desa MN, Muthanna A, Masri SN, Taib NM, Suhaili Z, Sulaiman N, Baharin NHZ, Shuan CY, Ariffin Z, Rahman NIA, Mohd Rani F, Palanisamy NK, Soh TST, Abdullah FH. Antimicrobial susceptibility, serotype distribution, virulence profile and molecular typing of piliated clinical isolates of pneumococci from east coast, Peninsular Malaysia. Sci Rep 2021; 11:8220. [PMID: 33859249 PMCID: PMC8050075 DOI: 10.1038/s41598-021-87428-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 03/30/2021] [Indexed: 12/14/2022] Open
Abstract
Pilus has been recently associated with pneumococcal pathogenesis in humans. The information regarding piliated isolates in Malaysia is scarce, especially in the less developed states on the east coast of Peninsular Malaysia. Therefore, we studied the characteristics of pneumococci, including the piliated isolates, in relation to antimicrobial susceptibility, serotypes, and genotypes at a major tertiary hospital on the east coast of Peninsular Malaysia. A total of 100 clinical isolates collected between September 2017 and December 2019 were subjected to serotyping, antimicrobial susceptibility test, and detection of pneumococcal virulence and pilus genes. Multilocus sequence typing (MLST) and phylogenetic analysis were performed only for piliated strains. The most frequent serotypes were 14 (17%), 6A/B (16%), 23F (12%), 19A (11%), and 19F (11%). The majority of isolates were resistant to erythromycin (42%), tetracycline (37%), and trimethoprim-sulfamethoxazole (24%). Piliated isolates occurred in a proportion of 19%; 47.3% of them were multidrug-resistant (MDR) and a majority had serotype 19F. This study showed ST236 was the most predominant sequence type (ST) among piliated isolates, which was related to PMEN clone Taiwan19F-14 (CC271). In the phylogenetic analysis, the piliated isolates were grouped into three major clades supported with 100% bootstrap values. Most piliated isolates belonged to internationally disseminated clones of S. pneumoniae, but pneumococcal conjugate vaccines (PCVs) have the potential to control them.
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Affiliation(s)
- Nurul Diana Dzaraly
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
| | - Mohd Nasir Mohd Desa
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia.
| | - AbdulRahman Muthanna
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
| | - Siti Norbaya Masri
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
| | - Niazlin Mohd Taib
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
| | - Zarizal Suhaili
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
- School of Animal Science, Aquatic Science and Environment, Faculty of Bioresources and Food Industry, Universiti Sultan Zainal Abidin, Besut Campus, Besut, Terengganu, Malaysia
| | - Nurshahira Sulaiman
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
| | - Nurul Hana Zainal Baharin
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
| | - Cheah Yun Shuan
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
| | - Zarina Ariffin
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
| | - Nor Iza A Rahman
- Faculty of Medicine, Universiti Sultan Zainal Abidin, Kuala Terengganu, Terengganu, Malaysia
| | - Farahiyah Mohd Rani
- Faculty of Medicine, Universiti Sultan Zainal Abidin, Kuala Terengganu, Terengganu, Malaysia
| | - Navindra Kumari Palanisamy
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, Universiti Teknologi MARA (UiTM), Sungai Buloh Campus, Jalan Hospital, Sungai Buloh, Selangor, Malaysia
| | - Tuan Suhaila Tuan Soh
- Department of Pathology, Sungai Buloh Hospital, Ministry of Health Malaysia, Jalan Hospital, Sungai Buloh, Selangor, Malaysia
| | - Fatimah Haslina Abdullah
- Department of Pathology, Sultanah Nur Zahirah Hospital, Ministry of Health Malaysia, Jalan Sultan Mahmud, Kuala Terengganu, Terengganu, Malaysia
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13
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Joshi SS, Al-Mamun MA, Weinberger DM. Correlates of Nonrandom Patterns of Serotype Switching in Pneumococcus. J Infect Dis 2021; 221:1669-1676. [PMID: 31875229 DOI: 10.1093/infdis/jiz687] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 12/23/2019] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Pneumococcus is a diverse pathogen, with >90 serotypes, each of which has a distinct polysaccharide capsule. Pneumococci can switch capsules, evading vaccine pressure. Certain serotype pairs are more likely to occur on the same genetic background as a results of serotype switching, but the drivers of these patterns are not well understood. METHODS We used the PubMLST and Global Pneumococcal Sequencing Project databases to quantify the number of genetic lineages on which different serotype pairs occur together. We also quantified the genetic diversity of each serotype. Regression model were used to evaluate the relationship between shared polysaccharide components and the frequency of serotype co-occurrence and diversity. RESULTS A number of serotype pairs occurred together on the same genetic lineage more commonly than expected. Co-occurrence of between-serogroup pairs was more common when both serotypes had glucose as a component of the capsule (and, potentially, glucuronic acid, any-N-acetylated sugar, or ribitol). Diversity also varied markedly by serotype and was associated with the presence of specific sugars in the capsule. CONCLUSIONS Certain pairs of serotypes are more likely to co-occur on the same genetic background. These patterns were correlated with shared polysaccharide components. This might reflect adaptation of strains to produce capsules with specific characteristics.
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Affiliation(s)
- Shreyas S Joshi
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Mohammad A Al-Mamun
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Daniel M Weinberger
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
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14
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Nzoyikorera N, Diawara I, Fresia P, Maaloum F, Katfy K, Nayme K, Maaloum M, Cornick J, Chaguza C, Timinouni M, Belabess H, Zerouali K, Elmdaghri N. Whole genomic comparative analysis of Streptococcus pneumoniae serotype 1 isolates causing invasive and non-invasive infections among children under 5 years in Casablanca, Morocco. BMC Genomics 2021; 22:39. [PMID: 33413118 PMCID: PMC7792055 DOI: 10.1186/s12864-020-07316-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 12/09/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Streptococcus pneumoniae serotype 1 remains a leading cause of invasive pneumococcal diseases, even in countries with PCV-10/PCV-13 vaccine implementation. The main objective of this study, which is part of the Pneumococcal African Genome project (PAGe), was to determine the phylogenetic relationships of serotype 1 isolates recovered from children patients in Casablanca (Morocco), compared to these from other African countries; and to investigate the contribution of accessory genes and recombination events to the genetic diversity of this serotype. RESULTS The genome average size of the six-pneumococcus serotype 1 from Casablanca was 2,227,119 bp, and the average content of coding sequences was 2113, ranging from 2041 to 2161. Pangenome analysis of the 80 genomes used in this study revealed 1685 core genes and 1805 accessory genes. The phylogenetic tree based on core genes and the hierarchical bayesian clustering analysis revealed five sublineages with a phylogeographic structure by country. The Moroccan strains cluster in two different lineages, the five invasive strains clusters altogether in a divergent clade distantly related to the non-invasive strain, that cluster with all the serotype 1 genomes from Africa. CONCLUSIONS The whole genome sequencing provides increased resolution analysis of the highly virulent serotype 1 in Casablanca, Morocco. Our results are concordant with previous works, showing that the phylogeography of S. pneumoniae serotype 1 is structured by country, and despite the small size (six isolates) of the Moroccan sample, our analysis shows the genetic cohesion of the Moroccan invasive isolates.
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Affiliation(s)
- Néhémie Nzoyikorera
- Department of Microbiology, Faculty of Medicine and Pharmacy of Casablanca, Hassan II University of Casablanca, Casablanca, Morocco.
- Bacteriology-Virology and Hospital Hygiene Laboratory, Ibn Rochd University Hospital Centre, Casablanca, Morocco.
| | - Idrissa Diawara
- Faculty of Sciences and Health Techniques, Mohammed VI University of Health Sciences (UM6SS) of Casablanca, Casablanca, Morocco
| | - Pablo Fresia
- Institut Pasteur de Montevideo, Pasteur + INIA Joint Unit (UMPI), Montevideo, Uruguay
- Institut Pasteur de Montevideo, Microbial Genomics Laboratory, Montevideo, Uruguay
| | - Fakhreddine Maaloum
- Department of Microbiology, Faculty of Medicine and Pharmacy of Casablanca, Hassan II University of Casablanca, Casablanca, Morocco
- Bacteriology-Virology and Hospital Hygiene Laboratory, Ibn Rochd University Hospital Centre, Casablanca, Morocco
| | - Khalid Katfy
- Department of Microbiology, Faculty of Medicine and Pharmacy of Casablanca, Hassan II University of Casablanca, Casablanca, Morocco
- Bacteriology-Virology and Hospital Hygiene Laboratory, Ibn Rochd University Hospital Centre, Casablanca, Morocco
| | - Kaotar Nayme
- Molecular Bacteriology Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Mossaab Maaloum
- Laboratory of Biology and Health, Faculty of Sciences Ben M'Sik, Hassan II University of Casablanca, Casablanca, Morocco
- Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Jennifer Cornick
- Malawi Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | | | - Mohammed Timinouni
- Molecular Bacteriology Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Houria Belabess
- Department of Microbiology, Faculty of Medicine and Pharmacy of Casablanca, Hassan II University of Casablanca, Casablanca, Morocco
- Bacteriology-Virology and Hospital Hygiene Laboratory, Ibn Rochd University Hospital Centre, Casablanca, Morocco
| | - Khalid Zerouali
- Department of Microbiology, Faculty of Medicine and Pharmacy of Casablanca, Hassan II University of Casablanca, Casablanca, Morocco
- Bacteriology-Virology and Hospital Hygiene Laboratory, Ibn Rochd University Hospital Centre, Casablanca, Morocco
| | - Naima Elmdaghri
- Department of Microbiology, Faculty of Medicine and Pharmacy of Casablanca, Hassan II University of Casablanca, Casablanca, Morocco
- Bacteriology-Virology and Hospital Hygiene Laboratory, Ibn Rochd University Hospital Centre, Casablanca, Morocco
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15
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Chaguza C, Heinsbroek E, Gladstone RA, Tafatatha T, Alaerts M, Peno C, Cornick JE, Musicha P, Bar-Zeev N, Kamng'ona A, Kadioglu A, McGee L, Hanage WP, Breiman RF, Heyderman RS, French N, Everett DB, Bentley SD. Early Signals of Vaccine-driven Perturbation Seen in Pneumococcal Carriage Population Genomic Data. Clin Infect Dis 2021; 70:1294-1303. [PMID: 31094423 PMCID: PMC7768739 DOI: 10.1093/cid/ciz404] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 05/15/2019] [Indexed: 11/14/2022] Open
Abstract
Background Pneumococcal conjugate vaccines (PCVs) have reduced pneumococcal diseases globally. Pneumococcal genomic surveys elucidate PCV effects on population structure but are rarely conducted in low-income settings despite the high disease burden. Methods We undertook whole-genome sequencing (WGS) of 660 pneumococcal isolates collected through surveys from healthy carriers 2 years from 13-valent PCV (PCV13) introduction and 1 year after rollout in northern Malawi. We investigated changes in population structure, within-lineage serotype dynamics, serotype diversity, and frequency of antibiotic resistance (ABR) and accessory genes. Results In children <5 years of age, frequency and diversity of vaccine serotypes (VTs) decreased significantly post-PCV, but no significant changes occurred in persons ≥5 years of age. Clearance of VT serotypes was consistent across different genetic backgrounds (lineages). There was an increase of nonvaccine serotypes (NVTs)—namely 7C, 15B/C, and 23A—in children <5 years of age, but 28F increased in both age groups. While carriage rates have been recently shown to remain stable post-PCV due to replacement serotypes, there was no change in diversity of NVTs. Additionally, frequency of intermediate-penicillin-resistant lineages decreased post-PCV. Although frequency of ABR genes remained stable, other accessory genes, especially those associated with mobile genetic element and bacteriocins, showed changes in frequency post-PCV. Conclusions We demonstrate evidence of significant population restructuring post-PCV driven by decreasing frequency of vaccine serotypes and increasing frequency of few NVTs mainly in children under 5. Continued surveillance with WGS remains crucial to fully understand dynamics of the residual VTs and replacement NVT serotypes post-PCV.
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Affiliation(s)
- Chrispin Chaguza
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge.,Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, United Kingdom.,Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre.,Darwin College, University of Cambridge, Silver Street, Cambridge
| | - Ellen Heinsbroek
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, United Kingdom.,HIV and STI Department, National Infection Service, Public Health England, London, United Kingdom
| | - Rebecca A Gladstone
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge
| | - Terence Tafatatha
- Malawi Epidemiology Intervention Research Unit (formerly KPS), Chilumba
| | - Maaike Alaerts
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre.,Center of Medical Genetics, University of Antwerp, Belgium
| | - Chikondi Peno
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre.,Medical Research Council Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, United Kingdom
| | - Jennifer E Cornick
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, United Kingdom.,Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre
| | - Patrick Musicha
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, United Kingdom.,Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre.,Mahidol Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand.,Nuffield Department of Medicine, University of Oxford, United Kingdom
| | - Naor Bar-Zeev
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, United Kingdom.,Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre.,Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Arox Kamng'ona
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, United Kingdom.,Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre.,Department of Biomedical Sciences, University of Malawi, College of Medicine, Blantyre
| | - Aras Kadioglu
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, United Kingdom
| | - Lesley McGee
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - William P Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | - Robert F Breiman
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia
| | - Robert S Heyderman
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre.,Division of Infection and Immunity, University College London, United Kingdom
| | - Neil French
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, United Kingdom.,Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre
| | - Dean B Everett
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre.,Medical Research Council Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, United Kingdom
| | - Stephen D Bentley
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge.,Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, United Kingdom.,Department of Pathology, University of Cambridge, United Kingdom
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16
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Hanachi M, Kiran A, Cornick J, Harigua-Souiai E, Everett D, Benkahla A, Souiai O. Genomic Characteristics of Invasive Streptococcus pneumoniae Serotype 1 in New Caledonia Prior to the Introduction of PCV13. Bioinform Biol Insights 2020; 14:1177932220962106. [PMID: 33088176 PMCID: PMC7545519 DOI: 10.1177/1177932220962106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 08/31/2020] [Indexed: 12/17/2022] Open
Abstract
Streptococcus pneumoniae serotype 1 is a common cause of global invasive pneumococcal disease. In New Caledonia, serotype 1 is the most prevalent serotype and led to two major outbreaks reported in the 2000s. The pneumococcal conjugate vaccine 13 (PCV13) was introduced into the vaccination routine, intending to prevent the expansion of serotype 1 in New Caledonia. Aiming to provide a baseline for monitoring the post-PCV13 changes, we performed a whole-genome sequence analysis on 67 serotype 1 isolates collected prior to the PCV13 introduction. To highlight the S. pneumoniae serotype 1 population structure, we performed a multilocus sequence typing (MLST) analysis revealing that NC serotype 1 consisted of 2 sequence types: ST3717 and the highly dominant ST306. Both sequence types harbored the same resistance genes to beta-lactams, macrolide, streptogramin B, fluoroquinolone, and lincosamide antibiotics. We have also identified 36 virulence genes that were ubiquitous to all the isolates. Among these virulence genes, the pneumolysin sequence presented an allelic profile associated with disease outbreaks and reduced hemolytic activity. Moreover, recombination hotspots were identified in 4 virulence genes and more notably in the cps locus (cps2L), potentially leading to capsular switching, a major mechanism of the emergence of nonvaccine types. In summary, this study represents the first overview of the genomic characteristics of S. pneumoniae serotype 1 in New Caledonia prior to the introduction of PCV13. This preliminary description represents a baseline to assess the impact of PCV13 on serotype 1 population structure and genomic diversity.
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Affiliation(s)
- Mariem Hanachi
- Laboratory of Bioinformatics, Biomathematics and Biostatistics-LR16IPT09, Institut Pasteur de Tunis, University of Tunis El Manar (UTM), Tunis, Tunisia.,Faculty of Science of Bizerte, University of Carthage, Jarzouna, Tunisia
| | - Anmol Kiran
- Queens Research Institute, University of Edinburgh, Edinburgh, UK.,Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Jennifer Cornick
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi.,Departement of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Emna Harigua-Souiai
- Laboratory of Molecular Epidemiology and Experimental Pathology-LR16IPT04, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - Dean Everett
- Queens Research Institute, University of Edinburgh, Edinburgh, UK.,Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Alia Benkahla
- Laboratory of Bioinformatics, Biomathematics and Biostatistics-LR16IPT09, Institut Pasteur de Tunis, University of Tunis El Manar (UTM), Tunis, Tunisia
| | - Oussama Souiai
- Laboratory of Bioinformatics, Biomathematics and Biostatistics-LR16IPT09, Institut Pasteur de Tunis, University of Tunis El Manar (UTM), Tunis, Tunisia.,Institut Supérieur des Technologies Médicales de Tunis, Université de Tunis El Manar, Tunis, Tunisia
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17
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Dzaraly ND, Muthanna A, Mohd Desa MN, Taib NM, Masri SN, Rahman NIA, Suhaili Z, Tuan Soh TS, Abdullah FH. Pilus islets and the clonal spread of piliated Streptococcus pneumoniae: A review. Int J Med Microbiol 2020; 310:151449. [PMID: 33092697 DOI: 10.1016/j.ijmm.2020.151449] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 08/17/2020] [Accepted: 08/24/2020] [Indexed: 12/11/2022] Open
Abstract
Pneumococci are a common cause of severe infections, such as otitis media, pneumonia, meningitis and bacteremia. Pili are detected in a small proportion of pneumococcal population, but these structures have recently been associated with bacterial virulence in humans. Therefore, the epidemiological relationships between pneumococcal pili, serotype and antimicrobial resistance are of interest. This study aims to discuss the virulence contribution of the Streptococcus pneumoniae pili and the epidemiological relationships among the pilus genes, antimicrobial resistance trends, regional serotypes and genotypic variations. Previous reports have characterized the pneumococcal pilus islet as a clonal feature in the pneumococcal serotypes that are covered by the pneumococcal conjugate vaccine (PCV), including serotypes 19A, 19F, 23F and 7F. Many of the pneumococcal molecular epidemiology network (PMEN) clones are piliated isolates that are also strongly associated with a high frequency of multidrug resistance. Most of these piliated pneumococcal isolates belong to a few clonal complexes (CC), such as CC320, CC199, CC271, CC191 and CC156. Additional molecular epidemiology and genomic studies, particularly whole genome sequence analysis (WGS), are needed to develop an in-depth understanding of the piliated pneumococcal isolates.
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Affiliation(s)
- Nurul Diana Dzaraly
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - AbdulRahman Muthanna
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Mohd Nasir Mohd Desa
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.
| | - Niazlin Mohd Taib
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Siti Norbaya Masri
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Nor Iza A Rahman
- Faculty of Medicine, Universiti Sultan Zainal Abidin, 21400, Kuala Terengganu, Terengganu, Malaysia
| | - Zarizal Suhaili
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia; School of Animal Sciences, Faculty of Bioresources and Food Industry, Universiti Sultan Zainal Abidin, Besut Campus, 22200, Besut, Terengganu, Malaysia; East Coast Environmental Research Institute, Universiti Sultan Zainal Abidin, Gong Badak Campus, 21300, Kuala Terengganu, Terengganu, Malaysia
| | - Tuan Suhaila Tuan Soh
- Department of Pathology, Sungai Buloh Hospital, Jalan Hospital, 47000, Sungai Buloh, Selangor, Malaysia
| | - Fatimah Haslina Abdullah
- Department of Pathology, Sultanah Nur Zahirah Hospital, Jalan Sultan Mahmud, 20400, Kuala Terengganu, Terengganu, Malaysia
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18
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Midouni Ayadi B, Mehiri E, Draoui H, Ghariani A, Essalah L, Raoult D, Fournier PE, Slim-Saidi LN. Phenotypic and molecular characterization of macrolide resistance mechanisms among Streptococcus pneumoniae isolated in Tunisia. J Med Microbiol 2020; 69:505-520. [PMID: 32159507 DOI: 10.1099/jmm.0.001151] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Introduction. Streptococcus pneumoniae is responsible for many community infections, with the main ones being pneumonia and meningitis. Pneumococcus has developed increased resistance to multiple classes of antibiotics. The evolution of antibiotic resistance in pneumococcus was influenced by changes in serotype distribution under vaccine selection pressure.Aim. The aim of this study was to determine the genes involved in macrolide resistance, the antimicrobial susceptibility, the serotype distribution and the spread of international antibiotic-resistant clones among clinical isolates of S. pneumoniae.Methodology. We investigated 86 erythromycin-resistant S. pneumoniae strains isolated from respiratory (n=74) or non-respiratory (n=12) samples in Tunisia. Antimicrobial susceptibility was tested using the disk diffusion method. Macrolide-resistant strains were analysed by polymerase chain reaction (PCR) for ermA, ermB, mefA and msrD. We also investigated the macrolide resistance mechanisms in eight isolates (9.3%) by sequencing the L4 and L22 riboprotein-coding genes, plus relevant segments of the three 23S rRNA genes. Capsular serotypes were detected by multiplex PCR. Sequence types (STs) were explored using multilocus sequence typing (MLST).Results. Among the 86 studied strains, 70 (81.4 %) were resistant to penicillin G. The prevalent serotypes were 19F, 14, 19A and 23F. We observed that the cMLSB phenotype (66/86, 76.7%) was the most common in these pneumococci. In addition, ermB was the most frequent resistance gene. No mutation in ribosomal protein L22 or L4 or 23S rRNA was detected. Overall, 44 STs were identified in this study, including 16 that were described for the first time. Resistance to lincomycin, tetracycline and trimethoprim/sulfamethoxazole was observed in 55 (64 %), 34 (39.5 %) and 31 (36 %) isolates, respectively. Furthermore, an increase in fluoroquinolone use in particular may lead to the emergence of levofloxacin-resistant strains. Multidrug resistance was observed in 83 isolates (96.5%). Three global antibiotic-resistant clones were identified: Denmark14 ST230, Portugal19F ST177 and Spain9V ST156.Conclusion. This study shows that macrolide resistance among S. pneumoniae isolated in Tunisia is mainly related to target site modification. Our observations demonstrate a high degree of genetic diversity and capsular types among strains resistant to macrolides.
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Affiliation(s)
- B Midouni Ayadi
- Aix Marseille University, IRD, SSA, Vitrome, IHU Mediterranee Infection, 19-21 Bd Jean Moulin, 13005 Marseille, France.,Microbiology Laboratory, A. Mami Hospital of Pneumology, UR12/SP18, Ariana, Tunisia.,Faculty of Sciences of Tunis - University of Tunis El Manar, Ariana, Tunisia
| | - E Mehiri
- Microbiology Laboratory, A. Mami Hospital of Pneumology, UR12/SP18, Ariana, Tunisia
| | - H Draoui
- Microbiology Laboratory, A. Mami Hospital of Pneumology, UR12/SP18, Ariana, Tunisia
| | - A Ghariani
- Microbiology Laboratory, A. Mami Hospital of Pneumology, UR12/SP18, Ariana, Tunisia
| | - L Essalah
- Microbiology Laboratory, A. Mami Hospital of Pneumology, UR12/SP18, Ariana, Tunisia
| | - D Raoult
- Aix Marseille University, IRD, Mephi, IHU Mediterranee Infection, 19-21 Bd Jean Moulin, 13005 Marseille, France
| | - P E Fournier
- Aix Marseille University, IRD, SSA, Vitrome, IHU Mediterranee Infection, 19-21 Bd Jean Moulin, 13005 Marseille, France
| | - L N Slim-Saidi
- Microbiology Laboratory, A. Mami Hospital of Pneumology, UR12/SP18, Ariana, Tunisia
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19
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Jacques LC, Panagiotou S, Baltazar M, Senghore M, Khandaker S, Xu R, Bricio-Moreno L, Yang M, Dowson CG, Everett DB, Neill DR, Kadioglu A. Increased pathogenicity of pneumococcal serotype 1 is driven by rapid autolysis and release of pneumolysin. Nat Commun 2020; 11:1892. [PMID: 32312961 PMCID: PMC7170840 DOI: 10.1038/s41467-020-15751-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 03/23/2020] [Indexed: 12/17/2022] Open
Abstract
Streptococcus pneumoniae serotype 1 is the predominant cause of invasive pneumococcal disease in sub-Saharan Africa, but the mechanism behind its increased invasiveness is not well understood. Here, we use mouse models of lung infection to identify virulence factors associated with severe bacteraemic pneumonia during serotype-1 (ST217) infection. We use BALB/c mice, which are highly resistant to pneumococcal pneumonia when infected with other serotypes. However, we observe 100% mortality and high levels of bacteraemia within 24 hours when BALB/c mice are intranasally infected with ST217. Serotype 1 produces large quantities of pneumolysin, which is rapidly released due to high levels of bacterial autolysis. This leads to substantial levels of cellular cytotoxicity and breakdown of tight junctions between cells, allowing a route for rapid bacterial dissemination from the respiratory tract into the blood. Thus, our results offer an explanation for the increased invasiveness of serotype 1. The mechanisms behind the high invasiveness of Streptococcus pneumoniae serotype 1 are unclear. Here, Jacques et al. show that this feature is due to overproduction and rapid release of pneumolysin, which induces cytotoxicity and breakdown of tight junctions, allowing rapid bacterial dissemination from the respiratory tract into the blood.
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Affiliation(s)
- Laura C Jacques
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Stavros Panagiotou
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Murielle Baltazar
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | | | - Shadia Khandaker
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Rong Xu
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Laura Bricio-Moreno
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Marie Yang
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | | | - Dean B Everett
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi, College of Medicine, Blantyre, Malawi
| | - Daniel R Neill
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Aras Kadioglu
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK.
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20
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Kalata NL, Nyazika TK, Swarthout TD, Everett D, French N, Heyderman RS, Gordon SB, Jambo KC. Pneumococcal pneumonia and carriage in Africa before and after introduction of pneumococcal conjugate vaccines, 2000-2019: protocol for systematic review. BMJ Open 2019; 9:e030981. [PMID: 31727654 PMCID: PMC6858229 DOI: 10.1136/bmjopen-2019-030981] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 10/18/2019] [Accepted: 10/21/2019] [Indexed: 12/18/2022] Open
Abstract
INTRODUCTION Africa harbours a high burden of pneumococcal disease, with associated high mortality rates. Despite 34 countries introducing the pneumococcal conjugate vaccine, which reduces the risk of pneumococcal carriage (a prerequisite for disease) of some of the most pathogenic pneumococcal serotypes, it remains uncertain whether they will achieve the sustained direct or indirect protection necessary to reduce pneumococcal carriage to levels sufficient to interrupt transmission and disease. We will therefore summarise the available data on the impact of the pneumococcal conjugate vaccine in reducing vaccine serotype carriage and pneumococcal pneumonia in Africa between 2000 and 2019. METHODS AND ANALYSIS Using a predetermined search strategy, we will conduct a comprehensive search of PubMed, MEDLINE database, the Excerpta Medica Database, the ISI Web of Science (Science Citation Index), Scopus and the African Index Medicus to identify published studies reporting the prevalence of Streptococcus pneumoniae carriage (vaccine type and non-vaccine type), incidence rates of pneumococcal pneumonia and mortality among children, adults and HIV-infected (all-ages) pre-pneumococcal conjugate vaccine (PCV) and post-PCV introduction (published between 1st January 2000 and 31st December 2019) in African countries that have introduced PCVs (PCV7/PCV10/PCV13) in their routine national immunisation programme. The studies retained and data extracted will be assessed for bias using prevalidated tools and checklists. Heterogeneity across studies will be assessed using the χ2 test on Cochrane Q statistic. A random effect meta-analysis will be used to estimate the overall prevalence of pneumococcal carriage and incidence of pneumococcal pneumonia across studies with similar characteristics. Results will be reported in compliance with the Meta-Analysis Of Observational Studies in Epidemiology guidelines. The protocol has been prepared in accordance to the 2015 guidelines on Preferred Reporting Items for Systematic Reviews and Meta-Analyses. ETHICS AND DISSEMINATION This systematic review will not require ethical approval as we will be using already published data. The final manuscript will be submitted for publication in a peer-reviewed journal and presented at conferences. PROSPERO REGISTRATION NUMBER CRD42019130976.
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Affiliation(s)
- Newton L Kalata
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - Tinashe K Nyazika
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Todd D Swarthout
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - Dean Everett
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
- The Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Neil French
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
- Centre for Global Vaccine Research, Institute of Infection and Global Health, Liverpool, UK
| | - Robert S Heyderman
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
- Division of Infection and Immunity, University College London, London, UK
| | - Stephen B Gordon
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Kondwani C Jambo
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
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21
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Clonal yet Different: Understanding the Causes of Genomic Heterogeneity in Microbial Species and Impacts on Public Health. mSystems 2019; 4:4/3/e00097-19. [PMID: 31219786 PMCID: PMC6533373 DOI: 10.1128/msystems.00097-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Why are members of a microbial species not the same? They may be clonal, but microbial populations are often composed of multiple cocirculating lineages distinguished by large phenotypic and genetic differences. Species and the mechanisms of speciation have been notoriously challenging to study in microbes owing to pervasive horizontal gene flow, widespread geographical distribution, and cryptic ecological niches that structure microbial populations. Understanding the origins of genomic variation in microbial species and populations is fundamental to questions critical to society and public health, such as "Are emerging diseases new species or variants of existing ones?," "What makes a resistant strain successful?," and "How will a pathogen respond to selective pressures?" To explore these questions, I use whole-genome sequencing of closely related strains to understand the evolutionary, ecological, and epidemiological dynamics of bacterial pathogens to inform effective, more precisely targeted public health interventions.
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22
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Whole-Genome Sequencing Analysis of Multidrug-Resistant Serotype 15A Streptococcus pneumoniae in Japan and the Emergence of a Highly Resistant Serotype 15A-ST9084 Clone. Antimicrob Agents Chemother 2019; 63:AAC.02579-18. [PMID: 30803976 DOI: 10.1128/aac.02579-18] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 02/13/2019] [Indexed: 11/20/2022] Open
Abstract
Since the introduction of pneumococcal conjugate vaccines (PCVs), an increase in the incidence of disease attributable to serotype 15A-ST63 (sequence type 63) pneumococci has been observed in many regions worldwide. We conducted a nationwide pediatric pneumococcal infection surveillance study between 2012 and 2014 in Japan. In the surveillance study, we detected multidrug-resistant serotype 15A-CC63 (clonal complex 63) strains (resistant to macrolides, penicillin, cefotaxime, and meropenem); in this study, we analyzed these resistant isolates to determine the dynamics and mechanism of resistance using whole-genome sequencing. In most of the penicillin-, cefotaxime-, and meropenem-resistant strains, recombination occurred in the pbp2x region, resulting in the acquisition of cefotaxime resistance in addition to penicillin and meropenem resistance. In the multidrug-resistant serotype 15A-CC63 strains, we identified a specific clone with ST9084, and all of the isolates were recovered from the Yamaguchi prefecture in Japan. All of the serotype 15A-ST9084 isolates had a novel pbp2x type (pbp2x-JP3) that was inserted by recombination events. The conserved amino acid motif profiles of pbp1a, pbp2b, and pbp2x of the strains were identical to those of serotype 19A-ST320. A Bayesian analysis-based date estimation suggested that this clone emerged in approximately 2002 before the introduction of the PCV in Japan. This clone should be monitored because serotype 15A is not contained in the currently used 13-valent PCV (PCV13), and it was resistant to beta-lactams, which are often used in a clinical setting.
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23
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Hiller NL, Sá-Leão R. Puzzling Over the Pneumococcal Pangenome. Front Microbiol 2018; 9:2580. [PMID: 30425695 PMCID: PMC6218428 DOI: 10.3389/fmicb.2018.02580] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 10/09/2018] [Indexed: 12/11/2022] Open
Abstract
The Gram positive bacterium Streptococcus pneumoniae (pneumococcus) is a major human pathogen. It is a common colonizer of the human host, and in the nasopharynx, sinus, and middle ear it survives as a biofilm. This mode of growth is optimal for multi-strain colonization and genetic exchange. Over the last decades, the far-reaching use of antibiotics and the widespread implementation of pneumococcal multivalent conjugate vaccines have posed considerable selective pressure on pneumococci. This scenario provides an exceptional opportunity to study the evolution of the pangenome of a clinically important bacterium, and has the potential to serve as a case study for other species. The goal of this review is to highlight key findings in the studies of pneumococcal genomic diversity and plasticity.
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Affiliation(s)
- N. Luisa Hiller
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, United States
- Center of Excellence in Biofilm Research, Allegheny Health Network, Pittsburgh, PA, United States
| | - Raquel Sá-Leão
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
- Departamento de Biologia Vegetal, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
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Bozio CH, Abdul-Karim A, Abenyeri J, Abubakari B, Ofosu W, Zoya J, Ouattara M, Srinivasan V, Vuong JT, Opare D, Asiedu-Bekoe F, Lessa FC. Continued occurrence of serotype 1 pneumococcal meningitis in two regions located in the meningitis belt in Ghana five years after introduction of 13-valent pneumococcal conjugate vaccine. PLoS One 2018; 13:e0203205. [PMID: 30192772 PMCID: PMC6128537 DOI: 10.1371/journal.pone.0203205] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 08/16/2018] [Indexed: 01/07/2023] Open
Abstract
Background Increases in pneumococcal meningitis were reported from Ghanaian regions that lie in the meningitis belt in 2016–2017, despite introduction of 13-valent pneumococcal conjugate vaccine (PCV13) in 2012 using a 3-dose schedule (6, 10, and 14 weeks). We describe pneumococcal meningitis epidemiology in the Ghanaian Northern and Upper West regions across two meningitis seasons. Methods Suspected meningitis cases were identified using World Health Organization standard definitions. Pneumococcal meningitis was confirmed if pneumococcus was the sole pathogen detected by polymerase chain reaction, culture, or latex agglutination in cerebrospinal fluid collected from a person with suspected meningitis during December 2015-March 2017. Pneumococcal serotyping was done using PCR. Annual age-specific pneumococcal meningitis incidence (cases per 100,000 population) was calculated, adjusting for suspected meningitis cases lacking confirmatory testing. Findings Among 153 pneumococcal meningitis cases, 137 (89.5%) were serotyped; 100 (73.0%) were PCV13-type, including 85 (62.0%) that were serotype 1, a PCV13-targeted serotype. Persons aged ≥5 years accounted for 96.7% (148/153) of cases. Comparing 2015–2016 and 2016–2017 seasons, the proportion of non-serotype 1 PCV13-type cases decreased from 20.0% (9/45) to 4.1% (3/74) (p = 0.008), whereas the proportion that was serotype 1 was stable (71.1% (32/45) vs. 58.1% (43/74); p = 0.16). Estimated adjusted pneumococcal meningitis incidence was 1.8 in children aged <5 years and ranged from 6.8–10.5 in older children and adults. Conclusions High pneumococcal meningitis incidence with a large proportion of serotype 1 disease in older children and adults suggests infant PCV13 vaccination has not induced herd protection with this schedule in this high-transmission setting.
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Affiliation(s)
- Catherine H. Bozio
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
- Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
- * E-mail:
| | | | | | | | | | | | - Mahamoudou Ouattara
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Velusamy Srinivasan
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Jeni T. Vuong
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - David Opare
- National Public Health Reference Laboratory, Ghana Health Service, Accra, Ghana
| | | | - Fernanda C. Lessa
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
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Use of Multiplex Quantitative PCR To Evaluate the Impact of Pneumococcal Conjugate Vaccine on Nasopharyngeal Pneumococcal Colonization in African Children. mSphere 2017; 2:mSphere00404-17. [PMID: 29134203 PMCID: PMC5677981 DOI: 10.1128/msphere.00404-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 10/13/2017] [Indexed: 11/20/2022] Open
Abstract
Pneumococcal conjugate vaccine (PCV) immunization of children induces shifts in colonizing pneumococcal serotypes. This study evaluated the effect of infant vaccination with 7-valent PCV (PCV7) on vaccine serotype (VT) colonization and whether the increase in nonvaccine serotype (NVT) was due to either unmasking of previously low-density-colonizing serotypes or increase in acquisition of NVT. A multiplex quantitative PCR (qPCR) was used to evaluate VT and NVT nasopharyngeal colonization in archived swabs of PCV-vaccinated and PCV-unvaccinated African children at 9 and 15 to 16 months of age. Molecular qPCR clearly identified the vaccine effect typified by a decrease in VT colonization and an increase in NVT colonization. Serotype 19A was primarily responsible for the higher NVT carriage among PCV vaccinees at 9 months of age (53.4% difference; P = 0.021) and 16 months of age (70.7% difference; P < 0.001). Furthermore, the density of serotype 19A colonization was higher in PCV-vaccinated groups than in PCV-unvaccinated groups (3.76 versus 2.83 CFU/ml [P = 0.046], respectively, and 4.15 versus 3.04 CFU/ml [P = 0.013], respectively) at 9 and 16 months of age, respectively. Furthermore, serotype 19A was also more commonly reported as a primary isolate (by having the highest density among other cocolonizing serotypes identified in the sample) in PCV7-vaccinated children, while being equally a primary (46.2%) or nonprimary (53.8%) isolate in PCV-unvaccinated children. Molecular qPCR showed both serotype replacement and unmasking to be the cause for the increase in NVT colonization in PCV7-vaccinated children, as some serotypes were associated with an absolute increase in colonization (replacement), while others were associated with an increase in detection (unmasking). IMPORTANCE This study focused on evaluating the effect of infant vaccination with 7-valent pneumococcal conjugate vaccine (PCV7), using a multiplex qPCR method, on the density of serotype-specific nasopharyngeal colonization in order to delineate the relative role of serotype replacement versus unmasking as the cause for the increase in nonvaccine serotype colonization in PCV7-vaccinated children. This is pertinent in the context of the ongoing deployment of PCV immunization in children, with surveillance of colonization considered an early proxy for disease that might arise from nonvaccine serotypes, as well as the success of childhood vaccination on indirect effect in the community through the interruption of pneumococcal transmission from vaccinated young children.
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